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Table 4 Mean branch lengths and node depths across clade resolution categories

From: What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades

Clade Type of node Number of nodes Mean branch length Standard error branch lengths Mean node depth Standard error node depth
Balistid fish Concordant 9 0.0113 0.0024 6.44 0.53
  mtDNA wins 3 0.0045 0.0021 6.33 0.84
  nucDNA wins 5 0.0042 0.0004 6.00 0.88
  Unique 6 0.0051 0.0005 3.00 0.73
Scarine fish Concordant 22 0.0110 0.0028 5.68 0.53
  mtDNA wins 10 0.0042 0.0040 6.90 0.95
  nucDNA wins 4 0.0058 0.0008 5.75 1.00
  Unique 4 0.0023 0.0007 6.75 1.97
Hemiphractid frogs Concordant 18 0.0528 0.0129 5.72 0.67
  mtDNA wins 13 0.0118 0.0019 8.85 1.36
  nucDNA wins 6 0.0142 0.0022 4.67 0.49
  Unique 3 0.0068 0.0007 8.00 1.00
Hylid frogs Concordant 41 0.0828 0.0081 10.12 0.63
  mtDNA wins 11 0.0686 0.0049 7.45 0.86
  nucDNA wins 13 0.0299 0.0150 9.46 1.11
  Unique 11 0.0196 0.0024 9.27 1.02
Plethodon salamanders Concordant 17 0.0199 0.0054 5.00 0.74
  mtDNA wins 25 0.0067 0.0020 8.32 1.93
  nucDNA wins 5 0.0052 0.0011 6.20 0.67
  Unique 4 0.0023 0.0003 8.25 1.11
Phrynosomatid lizards Concordant 17 0.1046 0.0169 5.29 0.73
  mtDNA wins 2 0.0221 0.0126 8.00 1.31
  nucDNA wins 12 0.0395 0.0091 7.92 3.00
  Unique 4 0.0152 0.0032 9.50 2.63
Alcid birds Concordant 14 0.0478 0.0093 3.71 0.40
  mtDNA wins 6 0.0212 0.0073 3.17 0.65
  nucDNA wins 1 0.0057 - 2.00 -
  Unique 0 - - - -
Caprimulgid birds Concordant 31 0.0562 0.0085 7.87 0.54
  mtDNA wins 10 0.0309 0.0042 8.40 0.99
  nucDNA wins 10 0.0149 0.0045 7.00 1.06
  Unique 4 0.0090 0.0023 8.00 0.82
Cotingid birds Concordant 22 0.0550 0.0081 5.27 0.52
  mtDNA wins 5 0.0132 0.0017 5.60 1.03
  nucDNA wins 7 0.0140 0.0029 5.29 1.15
  Unique 1 0.0091 - 1.00 -
Dicaeid birds Concordant 10 0.0919 0.0104 3.70 0.37
  mtDNA wins 13 0.0604 0.0042 5.54 1.49
  nucDNA wins 4 0.0312 0.0162 5.25 0.79
  Unique 1 0.0214 NA 5.00 NA
Emydid turtles Concordant 12 0.0078 0.0013 3.50 0.47
  mtDNA wins 7 0.0024 0.0004 6.29 0.88
  nucDNA wins 12 0.0032 0.0006 6.00 0.87
  Unique 5 0.0007 0.0002 7.80 1.39
Cervid mammals Concordant 7 0.0288 0.0030 2.57 0.43
  mtDNA wins 14 0.0160 0.0022 4.36 0.34
  nucDNA wins 2 0.0066 0.0014 4.00 3.00
  Unique 0 - - - -
Murid rodents (Philippines) Concordant 32 0.1341 0.0146 7.06 0.50
  mtDNA wins 7 0.1011 0.0083 6.71 0.89
  nucDNA wins 13 0.0494 0.0644 6.46 1.15
  Unique 3 0.0305 0.0065 3.67 1.20
Murid rodents (Sahul) Concordant 42 0.0097 0.0013 6.64 1.03
  mtDNA wins 4 0.0018 0.0003 9.50 4.75
  nucDNA wins 13 0.0038 0.0008 6.77 1.88
  Unique 1 0.0015 - 7.00 -
Pooled across clades Concordant 294 0.0556 0.0035 0.51 0.01
  mtDNA wins 130 0.0265 0.0045 0.60 0.02
  nucDNA wins 107 0.0198 0.0024 0.52 0.02
  Unique 47 0.0108 0.0015 0.53 0.04
  1. A summary of the mean branch lengths and mean node depths of branches in the combined-data trees for each clade, grouped by how they are resolved. For the node depths, larger numbers indicate shallower nodes (i.e. those closer to the tips and farther from the root). The last row of pooled data reports mean relative branch lengths and mean relative node depths. Significance testing is summarized in the Results and more extensively in Additional File 1.